Constructed wetlands (CWs) are a group of novel, natural wastewater treatment technologies which principally house microbes with help of plants and filter media. The denitrification rates in vertical flow constructed wetland (VFCW) are sensitive and in most cases complete nitrogen removal does not occur. In current study, two systems were evaluated, 1st was partial saturated up-flow VFCW and the 2nd was hybrid pilot scale setup of VFCW and floating treatment wetland (FTW) in series. Both these systems were implemented at single household scale for treatment of greywater. VFCW filter media were river sand and gravels with Canna indica as macrophyte. FTW rafts were made of thermocol sheets covering 100% of water surface in tank. System sampling was done for every 3rd day and pollutant removal performance was measured in terms of COD, total nitrogen (TN), ammoniacal nitrogen (NH4-N), nitrate (NO3-N), nitrite (NO2-N), and o-phosphate (PO4-P) concentrations of influent and effluent. Saturated VFCW system removed 89.09%, 78.7%, 67%, 68.74%, 94.6%, and 86.01% whereas hybrid wetland removed 91.5%, 92.32%, 82.2%, 71.13%, 97.25%, and 89.37% of COD, TN, NH4-N, NO3-N, NO2-N and PO4-P respectively. After stable pollutant removal trend, FTW macrophyte roots were harvested and subjected to metagenomic analysis on Illumina platform to identify microbial diversity and functional annotation related to nitrogen and phosphate removal. Microbial diversity showed Pseudomonas, Bacteroides, Clostridium, Azoarcus, Achromobacter as dominant top 5 genus. This group of genus highlights denitrifying microbial abundance greater than VFCW metagenomes microbial population. The presence of significantly higher denitrifying microbes in FTW confirms higher denitrification rate than VFCW, resulting in overall more Nitrogen removal by the system.